Could you please point out exactly where the problems happens ? I just had a quick check at KIAH now, but couldn't find any misplaced AIs.
Also, it's completely normal that, if you edit the AFCAD to change the parking type, GSX will still indicate the ones before modifications. This because the GSX .INI file will always automatically take priority over the AFCAD, otherwise you wouldn't be able to override anything.
If you update the ACAD, while the simulator itself ( that is, the AI system ) will use the new data, GSX will still use its .INI file that, if it was made starting with the original AFCAD supplied by FSDT (it surely is, if you don't do any changes), will still contain data from the original AFCAD so, when you edit the AFCAD, you should ALSO port all your changes to the GSX .INI file as well. There's no such thing as an automatic "sync" between GSX and the AFCAD.
This might possibly be also the cause of misplaced position, but ONLY if they affect the Warp Me or Reposition features in GSX. If you moved any parking spots in ADE, you are supposed to move them in GSX too, because GSX will always use its .INI, if there is one. But this won't affect AI, since AI don't know anything of the GSX .INI so if your problem are AI, IT IS AN AFCAD conflict, nothing that has anything to do with GSX, that's for sure,